The NPC pool spends for numbers. The GM reserve spends for plot.
There are two ways the GM can spend Fate Points on aspects in order to hit the PC's aspects or otherwise give them Fate Points.
Compels from the GM side - offering Fate Points for unfortunate plot directions to make perfect sense in light of PC or scene aspects, darn the luck - are proposed without cost and pay out from the unlimited GM reserve:
(from the SRD, Compelling Aspects)
[I]f a player wants to compel another character, it costs a fate point to propose the complication. The GM can always compel for free.
So if the GM's running a scene where the PCs are fighting Dark Stobolous in the engine room and things start going as they inevitably should, the GM can freely spend out of the NPC pool to boost Dark Stobolous's swings with the Fission Tulwar without worrying about saving a fate point to make a dubious escape in the chaos of the Self-Destructing Planet Cracker, darn the luck. That's a compel for a plot complication, so even though it benefits Dark Stobolous he doesn't have to pay because he's not a player - and because it hit a scene aspect to the PCs' detriment, they'll each get a Fate Point for taking the compel.
Invokes from the GM side - spending Fate Points to e.g. boost or reroll a die result - spend out of the scene NPC pool, even if there doesn't seem to be an NPC to spend it on. Let's say that you're running the players' escape as a scene, and in the course of it you realize that, hey, Starhound's Cleanly Severed Leg consequence (because the Fission Tulwar don't mess around) is going to make jumping the destroyed catwalk to the hanger more difficult.
But compels don't have numbers attached to them. They're about plot progression, through events and decisions. What are you going to compel Starhound to do, stay behind and die? You just want to make the jump harder! Well, remember the Bronze Rule: anything can be a character. And one of the standard uses of an invoke is to:
(from the SRD, Invoking Aspects)
Add +2 to any source of passive opposition, if it’s reasonable that the aspect you’re invoking could contribute to making things more difficult.
So, why not? The gap is just enough of a character that you can spend Fate Points out of the NPC pool to increase its passive opposition.